I don't think I understand this correctly: you reduced the bill payment by the amount of the materials the vendor 'purchased' from you? I would consider that a credit, not a purchase.  If that's the case, enter the vendor's bill for the full amount (materials kept included) and then enter a vendor credit for the amount of the materials the vendor 'purchased'.  Then, when you go to pay bills, you can apply the credit and QB will write a check for the remainder.